Multiple sequence alignment - TraesCS2A01G195400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G195400 chr2A 100.000 2959 0 0 1 2959 165103578 165106536 0.000000e+00 5465.0
1 TraesCS2A01G195400 chr2A 76.449 1363 222 52 710 2036 164866965 164868264 0.000000e+00 647.0
2 TraesCS2A01G195400 chr2A 82.914 755 93 19 1211 1957 165006971 165007697 0.000000e+00 647.0
3 TraesCS2A01G195400 chr2A 84.352 671 79 12 708 1368 164981213 164981867 4.160000e-178 634.0
4 TraesCS2A01G195400 chr2A 80.577 659 79 24 757 1397 164997651 164998278 2.080000e-126 462.0
5 TraesCS2A01G195400 chr2A 82.878 403 47 12 1545 1933 164982031 164982425 2.820000e-90 342.0
6 TraesCS2A01G195400 chr2A 89.062 128 14 0 2832 2959 559106545 559106672 3.050000e-35 159.0
7 TraesCS2A01G195400 chr2A 88.550 131 15 0 2829 2959 606776131 606776261 3.050000e-35 159.0
8 TraesCS2A01G195400 chr2A 83.750 160 17 6 2524 2680 165008729 165008882 3.070000e-30 143.0
9 TraesCS2A01G195400 chr2A 88.372 86 4 5 624 705 164866658 164866741 6.750000e-17 99.0
10 TraesCS2A01G195400 chr2A 97.561 41 1 0 1993 2033 164998678 164998718 1.470000e-08 71.3
11 TraesCS2A01G195400 chr1B 99.089 2964 22 2 1 2959 512050911 512053874 0.000000e+00 5319.0
12 TraesCS2A01G195400 chr2D 89.831 1593 94 32 709 2259 136515730 136514164 0.000000e+00 1982.0
13 TraesCS2A01G195400 chr2D 81.331 1307 163 40 708 1973 136523576 136522310 0.000000e+00 987.0
14 TraesCS2A01G195400 chr2D 87.964 673 47 21 708 1371 136634642 136633995 0.000000e+00 763.0
15 TraesCS2A01G195400 chr2D 76.535 1368 201 55 710 2036 136651662 136650374 3.220000e-179 638.0
16 TraesCS2A01G195400 chr2D 83.282 652 80 19 757 1397 136526368 136525735 9.200000e-160 573.0
17 TraesCS2A01G195400 chr2D 83.863 409 53 10 1545 1946 136612184 136611782 7.740000e-101 377.0
18 TraesCS2A01G195400 chr2D 78.720 578 68 33 1545 2108 136607753 136607217 4.730000e-88 335.0
19 TraesCS2A01G195400 chr2D 86.425 221 16 5 2257 2477 136514126 136513920 2.290000e-56 230.0
20 TraesCS2A01G195400 chr2D 75.787 508 70 24 1545 2042 136525738 136525274 1.070000e-49 207.0
21 TraesCS2A01G195400 chr2D 83.750 160 18 6 2524 2680 136516046 136515892 8.550000e-31 145.0
22 TraesCS2A01G195400 chr2D 88.235 68 6 2 627 694 136634845 136634780 2.440000e-11 80.5
23 TraesCS2A01G195400 chr2D 89.062 64 6 1 631 694 136651997 136651935 8.790000e-11 78.7
24 TraesCS2A01G195400 chr2B 89.002 1573 110 27 708 2259 194955072 194953542 0.000000e+00 1888.0
25 TraesCS2A01G195400 chr2B 91.096 438 28 4 2329 2760 194953416 194952984 1.530000e-162 582.0
26 TraesCS2A01G195400 chr2B 83.550 614 80 14 1485 2095 194997400 194996805 3.330000e-154 555.0
27 TraesCS2A01G195400 chr2B 84.655 580 48 19 813 1371 195167856 195167297 9.330000e-150 540.0
28 TraesCS2A01G195400 chr2B 82.609 644 74 11 764 1398 195060045 195059431 4.340000e-148 534.0
29 TraesCS2A01G195400 chr2B 79.595 642 90 23 1355 1973 195008341 195007718 3.530000e-114 422.0
30 TraesCS2A01G195400 chr2B 78.720 578 68 32 1545 2108 195059435 195058899 4.730000e-88 335.0
31 TraesCS2A01G195400 chr2B 84.674 261 32 5 1227 1486 194997696 194997443 1.360000e-63 254.0
32 TraesCS2A01G195400 chr2B 90.511 137 10 3 2123 2257 194996813 194996678 8.430000e-41 178.0
33 TraesCS2A01G195400 chr2B 84.277 159 18 6 2524 2680 194996340 194996187 6.610000e-32 148.0
34 TraesCS2A01G195400 chr2B 82.993 147 22 1 1552 1698 222586510 222586367 2.390000e-26 130.0
35 TraesCS2A01G195400 chr2B 92.308 52 4 0 643 694 195369226 195369175 1.140000e-09 75.0
36 TraesCS2A01G195400 chr2B 93.478 46 3 0 234 279 738164758 738164713 5.290000e-08 69.4
37 TraesCS2A01G195400 chrUn 100.000 418 0 0 2193 2610 477031178 477030761 0.000000e+00 773.0
38 TraesCS2A01G195400 chrUn 100.000 387 0 0 531 917 480490539 480490153 0.000000e+00 715.0
39 TraesCS2A01G195400 chr3B 86.154 195 25 2 1292 1486 462061457 462061265 2.990000e-50 209.0
40 TraesCS2A01G195400 chr7B 87.647 170 16 4 234 398 161239555 161239724 3.010000e-45 193.0
41 TraesCS2A01G195400 chr7B 81.034 174 28 5 413 584 658067475 658067305 1.850000e-27 134.0
42 TraesCS2A01G195400 chr1A 92.308 130 10 0 2830 2959 144510944 144510815 5.040000e-43 185.0
43 TraesCS2A01G195400 chr5D 84.492 187 27 2 399 584 520113776 520113961 1.810000e-42 183.0
44 TraesCS2A01G195400 chr5D 74.684 316 52 20 106 398 384884414 384884104 6.700000e-22 115.0
45 TraesCS2A01G195400 chr7A 86.207 174 15 6 234 398 206014895 206015068 2.340000e-41 180.0
46 TraesCS2A01G195400 chr5A 91.538 130 11 0 2830 2959 634467702 634467831 2.340000e-41 180.0
47 TraesCS2A01G195400 chr5A 90.769 130 12 0 2830 2959 401507635 401507506 1.090000e-39 174.0
48 TraesCS2A01G195400 chr5A 89.922 129 13 0 2831 2959 184015980 184016108 1.820000e-37 167.0
49 TraesCS2A01G195400 chr5A 89.844 128 13 0 2832 2959 407785349 407785476 6.560000e-37 165.0
50 TraesCS2A01G195400 chr3D 88.636 132 13 2 2829 2959 166942915 166943045 3.050000e-35 159.0
51 TraesCS2A01G195400 chr1D 84.024 169 23 4 234 398 262304655 262304823 3.050000e-35 159.0
52 TraesCS2A01G195400 chr1D 93.204 103 7 0 59 161 463469573 463469675 5.110000e-33 152.0
53 TraesCS2A01G195400 chr4D 88.506 87 8 2 41 126 468902025 468901940 1.450000e-18 104.0
54 TraesCS2A01G195400 chr4D 90.909 55 5 0 169 223 468901984 468901930 1.140000e-09 75.0
55 TraesCS2A01G195400 chr5B 96.970 33 1 0 184 216 434512987 434512955 4.120000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G195400 chr2A 165103578 165106536 2958 False 5465.000000 5465 100.000000 1 2959 1 chr2A.!!$F1 2958
1 TraesCS2A01G195400 chr2A 164981213 164982425 1212 False 488.000000 634 83.615000 708 1933 2 chr2A.!!$F5 1225
2 TraesCS2A01G195400 chr2A 165006971 165008882 1911 False 395.000000 647 83.332000 1211 2680 2 chr2A.!!$F7 1469
3 TraesCS2A01G195400 chr2A 164866658 164868264 1606 False 373.000000 647 82.410500 624 2036 2 chr2A.!!$F4 1412
4 TraesCS2A01G195400 chr2A 164997651 164998718 1067 False 266.650000 462 89.069000 757 2033 2 chr2A.!!$F6 1276
5 TraesCS2A01G195400 chr1B 512050911 512053874 2963 False 5319.000000 5319 99.089000 1 2959 1 chr1B.!!$F1 2958
6 TraesCS2A01G195400 chr2D 136513920 136516046 2126 True 785.666667 1982 86.668667 709 2680 3 chr2D.!!$R3 1971
7 TraesCS2A01G195400 chr2D 136522310 136526368 4058 True 589.000000 987 80.133333 708 2042 3 chr2D.!!$R4 1334
8 TraesCS2A01G195400 chr2D 136633995 136634845 850 True 421.750000 763 88.099500 627 1371 2 chr2D.!!$R5 744
9 TraesCS2A01G195400 chr2D 136650374 136651997 1623 True 358.350000 638 82.798500 631 2036 2 chr2D.!!$R6 1405
10 TraesCS2A01G195400 chr2D 136607217 136607753 536 True 335.000000 335 78.720000 1545 2108 1 chr2D.!!$R1 563
11 TraesCS2A01G195400 chr2B 194952984 194955072 2088 True 1235.000000 1888 90.049000 708 2760 2 chr2B.!!$R6 2052
12 TraesCS2A01G195400 chr2B 195167297 195167856 559 True 540.000000 540 84.655000 813 1371 1 chr2B.!!$R2 558
13 TraesCS2A01G195400 chr2B 195058899 195060045 1146 True 434.500000 534 80.664500 764 2108 2 chr2B.!!$R8 1344
14 TraesCS2A01G195400 chr2B 195007718 195008341 623 True 422.000000 422 79.595000 1355 1973 1 chr2B.!!$R1 618
15 TraesCS2A01G195400 chr2B 194996187 194997696 1509 True 283.750000 555 85.753000 1227 2680 4 chr2B.!!$R7 1453

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
438 443 1.290324 CTGTGGACACGGGTGAGAG 59.710 63.158 0.00 0.0 34.12 3.20 F
2037 5504 2.202479 GGAGATGCGCCGTTTTGC 60.202 61.111 4.18 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 5076 1.024271 GTGGTTGCTGCAGAACAAGA 58.976 50.000 20.43 0.0 0.0 3.02 R
2909 6942 2.202797 CGCCAGATGAGGACGTGG 60.203 66.667 0.00 0.0 0.0 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
438 443 1.290324 CTGTGGACACGGGTGAGAG 59.710 63.158 0.00 0.0 34.12 3.20
2037 5504 2.202479 GGAGATGCGCCGTTTTGC 60.202 61.111 4.18 0.0 0.00 3.68
2610 6641 1.302033 CCTCCTGCCACAGTGACAC 60.302 63.158 0.62 0.0 0.00 3.67
2860 6893 1.391144 GCAAAATTGCGTCTGGAATGC 59.609 47.619 1.90 0.0 45.11 3.56
2909 6942 2.470286 CGTTTTCTCGCTGTCCGC 59.530 61.111 0.00 0.0 36.73 5.54
2931 6964 3.785859 TCCTCATCTGGCGGCCAC 61.786 66.667 19.77 0.0 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.812499 CGTCCGGGGATGAACGAT 59.188 61.111 0.00 0.00 37.31 3.73
421 426 2.207229 CCTCTCACCCGTGTCCACA 61.207 63.158 0.00 0.00 0.00 4.17
438 443 1.235281 ACCTCGCGCCTTCTTTTTCC 61.235 55.000 0.00 0.00 0.00 3.13
1657 5076 1.024271 GTGGTTGCTGCAGAACAAGA 58.976 50.000 20.43 0.00 0.00 3.02
2037 5504 7.519970 GCTTAGAGTAGCAGAGTAAGAGCTAAG 60.520 44.444 0.00 0.00 41.96 2.18
2191 5681 1.471119 AGCTGCTGCATGCTACAAAT 58.529 45.000 20.33 5.42 43.37 2.32
2610 6641 2.271800 GGTTAAGTCGTGGAGATGCTG 58.728 52.381 0.00 0.00 0.00 4.41
2902 6935 2.890847 GATGAGGACGTGGCGGACAG 62.891 65.000 0.00 0.00 0.00 3.51
2909 6942 2.202797 CGCCAGATGAGGACGTGG 60.203 66.667 0.00 0.00 0.00 4.94


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.